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<p class="pageName">Realease notes</p>



<h3><u>P<sup>3</sup>DB version 1.2 (May 2010)</u></h3>
<ul>
        <li>
            In P<sup>3</sup>DB version 1.2, two phosphorylation datasets on <i>Medicago truncatula</i> 
			(<a href="http://www.ncbi.nlm.nih.gov/pubmed/19923235">Grimsrud et al. (2009)</a>)
			and <i>Oryza sativa</i> (<a href="http://www.ncbi.nlm.nih.gov/pubmed/20466843">Nakagami et al. 2010</a>)
            were deposited.
        </li>
		<li>
			All low-resolution phosphoproteomics data were removed.
		</li>

</ul>

<h3><u>P<sup>3</sup>DB version 1.1 (September 2008)</u></h3>
<ul>
        <li>
            In P<sup>3</sup>DB version 1.1, another phosphorylation dataset on <i>Arabidopsis thaliana</i> 
            from <a href="http://www.nature.com/msb/journal/v4/n1/full/msb200832.html">Sugiyama et al., 2008</a> 
            was deposited.
        </li>
        <li>
            The dataset includes 2172 phosphorylation sites, out of which,
            85.0, 10.7, and 4.3% are phospho-serines, 
            phospho-threonines and phospho-tyrosine respectively.
        </li>

</ul>

<h3><u>P<sup>3</sup>DB version 1.0 (June 2008)</u></h3>
<ul>
        <li>
            P<sup>3</sup>DB version 1.0 was constructed with a dataset from oilseed rape (<i>Brassica napus</i> var. Reston)
            developing seed obtained using a combination of data-dependent neutral loss and multistage
            activation mass spectrometry. 
        </li>
        <li>
            The dataset includes 14 670 non-redundant phosphorylation sites
            from 8,894 phosph-peptides in 6,382 substrate proteins.
            Out of these 14 670 phosphorylation sites, 8350 (57%) are phospho-serines,
            4753 (32%) are phospho-threonines and 1567 (11%) are phospho-tyrosine.
			<font color="red">(This low-resolution data has been removed.)</font>
        </li>
        <!--li> Experiment setting: 
          <ul>
             <li>All samples prepared from developing seed of canola at 4 weeks after flowering were analyzed by <b> LC-MS/MS on a linear ion trap
                 ProteomeX LTQ workstation (Thermo-Finnigan, San Jose, CA) using CID and MSA or DDNLMS3 method</b>.</li>
             <li>Five data-dependent MS/MS scans [isolation width 2 amu, 35% normalized collision energy, minimum signal threshold 500 counts, 
                 dynamic exclusion (repeat count, 1; repeat duration, 30 sec; exclusion duration, 60 sec)] of the five most intense parent
                 ions were acquired in a positive acquisition mode following each full scan (mass range m/z 400 – 2000).</li>
             <li>Acquired MS spectra were searched against the indexed plant database (keywords: <i>Arabidopsis; Brassica; Glycine; Medicago;
                 Oryza; and Zea</i>) using the BioWorks 3.2SR1 software which utilizes the SEQUEST algorithm for processing the raw data.</li>
             <li>The indexed database contained a static modification of +57 Da (carboxyamidomethylation) on cysteine and differential 
                 modifications of +16 Da (oxidation) on methionine and +80 Da on serine, threonine, and tyrosine residues.</li>
             <li>The search parameters for this database were set as follows:
                 <ol>
                 <li>enzyme: trypsin;</li>
                 <li>number of internal cleavage sites: 2;</li>
                 <li>mass range: 400 – 4000;</li>
                 <li>threshold: 500;</li>
                 <li>minimum ion count: 35;</li>
                 <b><li>peptide mass tolerance: 1.0.</li></b>
                 </ol>
             </li>
             <li>To obtain high-confidence and unambiguous peptide and protein assignments, the following criteria were applied:
                  <b>
                  <ol>
                  <li>a peptide correlation score (XCorr) of at least 1.9, 2.5, and 3.3 for +1, +2, and +3 charged ions, respectively;</li>
                  <li>a peptide probability of equal or lower than 0.05.  A peptide probability of 0.05 provides a minimum of 98.5% confidence
                      on the peptide assignment.</li>
                  </ol>
                  </b>
             </li>
          </ul>
        </li>
        <li>
            Note: since the genome information of oilseed rape is limited, when searching for protein to match the
            phospho-peptides, we use NCBI protein database by selecting proteins of the following plant species <i>Arabidopsis thaliana</i>,
            <i>Oryza sativa</i>, <i>Zea mays</i>, <i>Brassica rapa</i>, <i>Brassica napus</i>, <i>Brassica carinata</i>,
            <i>Brassica juncea</i>, <i>Brassica oleracea</i>, <i>Brassica tournefortii</i>, <i>Medicago truncatula</i>,
            <i>Medicago sativa</i> and <i>Glycine max</i>. For this reason, P<sup>3</sup>DB v1.0 has phosphorylation proteins in all
            these species, but the source organism for all phospho-peptides in v1.0 are oilseed rape (<i>Brassica napus</i> var. Reston).
        </li>
        <li>
            The status of Brassica genome is available on <a href="http://brassica.bbsrc.ac.uk/">Brassica Genome Gateway</a> and
			<a href="http://rapeseed.plantsignal.cn/">Shanghai Rapeseed Database</a>.
        </li-->

</ul>

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